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We have developed a new chemical patterning technique based on standard lithography-based processes to assemble nanostructures on surfaces with extraordinarily high selectivity. This patterning process is used to create patterns of aminosilane molecular layers surrounded by highly inert poly (ethylene glycol) (PEG) molecules. While the aminosilane regions facilitate nanostructure assembly, the PEG coating prevents adsorption of molecules and nanostructures, thereby priming the semiconductor substrate for the highly localized and programmed assembly of nanostructures. We demonstrate the power and versatility of this manufacturing process by building multilayered structures of gold nanoparticles attached to molecules of DNA onto the aminosilane patterns, with zero nanocrystal adsorption onto the surrounding PEG regions. The highly specific surface chemistry developed here can be used in conjunction with standard microfabrication and emerging nanofabrication technology to seamlessly integrate various nanostructures with semiconductor electronics.